15-80397045-T-C

Position:

• chr15-80397045-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_184068.1(ARNT2-DT):​n.353+899A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,994 control chromosomes in the GnomAD database, including 9,066 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.33 (9066 hom., cov: 31)
• Consequence: ARNT2-DT NR_184068.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.70

Genes affected

ARNT2-DT (HGNC:56077): (ARNT2 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ARNT2-DT	NR_184068.1	n.353+899A>G		intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184067.1	n.635+899A>G		intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184069.1	n.635+899A>G		intron_variant, non_coding_transcript_variant
ARNT2-DT	NR_184070.1	n.353+899A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ARNT2-DT	ENST00000656160.1	n.653+899A>G		intron_variant, non_coding_transcript_variant
ARNT2-DT	ENST00000559008.2	n.137+899A>G		intron_variant, non_coding_transcript_variant		3
ARNT2-DT	ENST00000559267.1	n.64+899A>G		intron_variant, non_coding_transcript_variant		2
ARNT2-DT	ENST00000653750.1	n.365+899A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49586 AN: 151876 Hom.: 9069 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.331

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.326 AC: 49584 AN: 151994 Hom.: 9066 Cov.: 31 AF XY: 0.330 AC XY: 24509 AN XY: 74292

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.329

Alfa AF: 0.343 Hom.: 3849

Bravo AF: 0.311

Asia WGS AF: 0.483 AC: 1678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.071
DANN	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17223788; hg19: chr15-80689387;